Background: Tetracentron sinense Oliv. is an ancient relict species in the family Trochodendraceae and a national secondary-level conservation plant in China. It is listed in Appendix III of the Convention of International Trade of Endangered Species, making its international trade subject to regional control. Knowledge of the spatial genetic structure (SGS) of the natural population of T. sinense is of great significance for the effective protection and management of its germplasm resource. Methods: Fifteen pairs of microsatellite primers were used to analyze the fine-scale SGS and gene flow of the national population of T. sinense in Leigong Mountain National Nature Reserve (LGM). Results: Compared with that of other endangered plants, the fine-scale genetic diversity of the T. sinense population was at the middle level. The genetic diversity levels in the four patches of T. sinense were different, resulting in significant genetic differentiation (Fst = 0.071–0.098), and the fine-scale genetic variation of the population was mainly from within patches. There was a significant SGS in the T. sinense population within a range of 400 m, and the quantified Sp value of the SGS was 0.0305. The gene flow of T. sinense in LGM was greatly restricted, and the distance of gene diffusion decreased with an increase in the effective density of the T. sinense population. Conclusions: The T. sinense population in LGM is suffering from the risk of inbreeding decline, and its limited gene flow will increase the accumulation of this risk. The spatial range of its genetic structure is within 20 m, and the individuals are closely related in this range. Therefore, the sampling interval for individuals during ex situ conservation should be 20 m apart to ensure that the collected individuals can exhibit more complete genetic variation. © 2023 The Authors